Properties of neutrality tests based on allele frequency spectrum

One of the main necessities for population geneticists is the availability of statistical tools that enable to accept or reject the neutral Wright-Fisher model with high power. A number of statistical tests have been developed to detect specific deviations from the null frequency spectrum in different directions (i.e., Tajima's D, Fu and Li's F and D test, Fay and Wu's H). Recently, a general framework was proposed to generate all neutrality tests that are linear functions of the frequency spectrum. In this framework, a family of optimal tests was developed to have almost maximum power against a specific alternative evolutionary scenario. Following these developments, in this paper we provide a thorough discussion of linear and nonlinear neutrality tests. First, we present the general framework for linear tests and emphasize the importance of the property of scalability with the sample size (that is, the results of the tests should not depend on the sample size), which, if missing, can guide to errors in data interpretation. The motivation and structure of linear optimal tests are discussed. In a further generalization, we develop a general framework for nonlinear neutrality tests and we derive nonlinear optimal tests for polynomials of any degree in the frequency spectrum.Comment: 42 pages, 3 figures, elsarticl

Intermolecular interactions in eumelanins: A computational bottom-up approach. I. small building blocks

The non-covalent interactions between pairs of the smallest eumelanins building blocks, 5,6-dihydroxy-indole (DHI) and its redox derivatives, are subjected to a systematic theoretical investigation, elucidating their nature and commenting on some of their possible effects on the layered structure of eumelanin. An accurate yet feasible protocol, based on second order perturbation theory, was set up and validated herein, and thereafter used to sample the intermolecular potential energy surfaces of several DHI related dimers. From the analysis of the resulting local minima, the crucial role of stacking interactions is assessed, evidencing strong effects on the geometrical arrangement of the dimer. Furthermore, the absorption spectra of the considered dimers in their most stable arrangements are computed and discussed in relation to the well known eumelanin broadband features. The present findings may help in elucidating several eumelanin features, supporting the recently proposed geometrical order/disorder model (Chen et al., Nat. Commun. 2014, 5, 3859)

Predicting light absorption properties of anthocyanidins in solution: a multi-level computational approach

A multi-level computational protocol is devised to calculate the absorption spectra in ethanol solution of a series of anthocyanidins relevant for dye-sensitized solar cells. The protocol exploits the high accuracy of second-order multi-reference perturbation theory to correct the results of the more feasible TD-DFT calculations, which were performed on hundreds of configurations sampled from molecular dynamics (MD) trajectories. The latter were purposely carried out with accurate and reliable force fields, specifically parameterized against quantum mechanical data, for each of the investigated dyes. Besides yielding maximum absorption wavelengths very close to the experimental values, the present approach was also capable of predicting reliable band shapes, even accounting for the subtle differences observed along the homolog series. Finally, the atomistic description achieved by MD simulations allowed for a deep insight into the different micro-solvation patterns around each anthocyanidin and their effects on the resulting dye’s properties. This work can be considered as a step toward the implementation of a computational protocol able to simulate the whole system formed by the organic dye and its heterogeneous embedding that constitutes dye-sensitized solar cells

Perturbative multireference configuration interaction (CI-MRPT2) calculations in a focused dynamical approach: A computational study of solvatochromism in pyrimidine

We have investigated solvatochromic effects over a solvent series of increasing polarity on the prototype molecule pyrimidine as a solute species. The line shape profiles, obtained by a time-dependent approach based on quantum mechanical calculations performed over frames sampled from classical molecular dynamics trajectories, were directly compared to the available experimental bands. The multireference configuration interaction second-order perturbation (CI-MRPT2) calculations are in quantitative agreement with the experiment. The results also confirm how nonprotic solvents can be confidently modeled by continuous solvation models as the polarizable continuum model, whereas protic solvents, as water, require the inclusion of explicit solvent molecules to account for the effects of hydrogen bonds

The phenoxyl group-modulated interplay of cation-π and σ-type interactions in the alkali metal series.

An extensive exploration of the interaction PESs of phenol and catechol complexes with alkali metal cations reveals a striking effect of –OH substitution on the balance between cation-π and σ-type noncovalent interactions

Quantitative prediction and interpretation of spin energy gaps in polyradicals: the virtual magnetic balance

Open-shell organic molecules possessing more than two unpaired electrons and sufficient stability even at room temperature are very unusual, but few were recently synthesized that promise a number of fascinating applications. Unfortunately, reliable structural information is not available and only lower limits can be estimated for energy splittings between the different spin states. On these grounds, we introduce here an effective ‘virtual magnetic balance’, a robust and user-friendly tool purposely tailored for polyradicals and devised to be used in parallel with experimental studies. The main objective of this tool is to provide reliable structures and quantitative splittings of spin states of large, complex molecules. We achieved this objective with reasonable computation times and in a theoretical framework that allows disentanglement of different stereo-electronic effects contributing to the overall experimental result. A recently synthesized tetraradical with remarkable chemical stability was used as a case study

Magnetic gaps in organic tri-radicals: From a simple model to accurate estimates

The calculation of the energy gap between the magnetic states of organic poly-radicals still represents a challenging playground for quantum chemistry, and high-level techniques are required to obtain accurate estimates. On these grounds, the aim of the present study is twofold. From the one side, it shows that, thanks to recent algorithmic and technical improvements, we are able to compute reliable quantum mechanical results for the systems of current fundamental and technological interest. From the other side, proper parameterization of a simple Hubbard Hamiltonian allows for a sound rationalization of magnetic gaps in terms of basic physical effects, unraveling the role played by electron delocalization, Coulomb repulsion, and effective exchange in tuning the magnetic character of the ground state. As case studies, we have chosen three prototypical organic tri-radicals, namely, 1,3,5-trimethylenebenzene, 1,3,5-tridehydrobenzene, and 1,2,3-tridehydrobenzene, which differ either for geometric or electronic structure. After discussing the differences among the three species and their consequences on the magnetic properties in terms of the simple model mentioned above, accurate and reliable values for the energy gap between the lowest quartet and doublet states are computed by means of the so-called difference dedicated configuration interaction (DDCI) technique, and the final results are discussed and compared to both available experimental and computational estimates

Noncovalent Interactions in the Catechol Dimer

Noncovalent interactions play a significant role in a wide variety of biological processes and bio-inspired species. It is, therefore, important to have at hand suitable computational methods for their investigation. In this paper, we report on the contribution of dispersion and hydrogen bonds in both stacked and T-shaped catechol dimers, with the aim of delineating the respective role of these classes of interactions in determining the most stable structure. By using second-order Møller–Plesset (MP2) calculations with a small basis set, specifically optimized for these species, we have explored a number of significant sections of the interaction potential energy surface and found the most stable structures for the dimer, in good agreement with the highly accurate, but computationally more expensive coupled cluster single and double excitation and the perturbative triples (CCSD(T))/CBS) method

DCF Data Call Coverage Report for the Mediterranean and Black Sea in 2014

DG Mare called the DCF Data from Member States in the Mediterranean and Black Sea on April 2014, defining the deadline of 9 June 2014 for data submissions from member states, under the Community Framework of Data Collection Regulation (DCR) (Council Regulation (EC) № 199/2008 of 25th February 2008). A second deadline specific for the Black Sea was established on 8 September 2014. The data call also defined a third deadline 12 January 2015 for the submission of trawl surveys data for Mediterranean MS. aruptii. The DCF data submitted by national correspondents are duly evaluated in the present coverage report by JRC DCF team as part of an Administrative Arrangement with DG MARE. The report provides a detailed review of the timeliness and completeness of data submissions by Member States.JRC.G.3-Maritime affair

Cr6+ adsorption by modified vermiculite

This work aimed at investigating the adsorption of Cr6+ in water by exfoliated vermiculite. The adsorbant tested in this experiment was a vermiculite (from China) which has been subjected to heating at 1000 °C for 1 minute, resulting in an exfoliated vermiculite. Three effects were studied: 1) contact time; 2) initial concentracion of Cr6+; 3) adsorbent mass. Samples were analysed by X Ray Fluorescence (XRF), X Ray Diffraction (XRD) and the solutions with Inductively Coupled Plasma Mass Spectrometry (ICP-MS) to quantify the adsorbed Cr6+ by the vermiculite. Results from XRD diffraction showed a conversion of vermiculite into flogopite after heating at 1000°C for 1 minute because of: 1) high content of potassium, 2) dehydration and 3) structural re-ordering; after the contact of vermiculite with Cr6+, the mineral structure did not change. The adsorption of Cr6+ was studied by Langmuir, Freundlich and Dubinin-Kaganer-Radushkevich (DKR) isotherm models. DKR model, indicative of a cooperative process, described adsorption equilibrium better than the other two models and the maximum adsorption capacity obtained was of 2.81 mol/g. Kinetic was studied using pseudo-first and pseudo-second order kinetic models, with a better description of the process by pseudo-second order model with correlation coefficient almost unitary (R2=0.9984; other kinetic parameters were k2=0.0015 and the absorption initial rate of 0.2x10-8 mg g-1 h-1). The present study demonstrates the effectiveness of modified vermiculite adsorbents for the treatment of hexavalent chromium-contaminated waters and that its adsorption depends on the experimental conditions (such as contact time, initial concentracion of Cr6+ and adsorbent mass)